In your stylesheet:
your header has a defined background of:
background: #ebeaf5 url('images/logo.gif') no-repeat left;
If you delete that from your style.css, you won't have the problem with duplicate images for your header.
Since you have that defined background image PLUS
<a href="http://noncollective.com"><img src="http://noncollective.com/wp-content/themes/noncollective/images/logo.gif"></a>
already in your HTML, you're getting "duplicate" images.